1
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Kars ME, Wu Y, Stenson PD, Cooper DN, Burisch J, Peter I, Itan Y. The landscape of rare genetic variation associated with inflammatory bowel disease and Parkinson's disease comorbidity. Genome Med 2024; 16:66. [PMID: 38741190 DOI: 10.1186/s13073-024-01335-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD) and Parkinson's disease (PD) are chronic disorders that have been suggested to share common pathophysiological processes. LRRK2 has been implicated as playing a role in both diseases. Exploring the genetic basis of the IBD-PD comorbidity through studying high-impact rare genetic variants can facilitate the identification of the novel shared genetic factors underlying this comorbidity. METHODS We analyzed whole exomes from the BioMe BioBank and UK Biobank, and whole genomes from a cohort of 67 European patients diagnosed with both IBD and PD to examine the effects of LRRK2 missense variants on IBD, PD and their co-occurrence (IBD-PD). We performed optimized sequence kernel association test (SKAT-O) and network-based heterogeneity clustering (NHC) analyses using high-impact rare variants in the IBD-PD cohort to identify novel candidate genes, which we further prioritized by biological relatedness approaches. We conducted phenome-wide association studies (PheWAS) employing BioMe BioBank and UK Biobank whole exomes to estimate the genetic relevance of the 14 prioritized genes to IBD-PD. RESULTS The analysis of LRRK2 missense variants revealed significant associations of the G2019S and N2081D variants with IBD-PD in addition to several other variants as potential contributors to increased or decreased IBD-PD risk. SKAT-O identified two significant genes, LRRK2 and IL10RA, and NHC identified 6 significant gene clusters that are biologically relevant to IBD-PD. We observed prominent overlaps between the enriched pathways in the known IBD, PD, and candidate IBD-PD gene sets. Additionally, we detected significantly enriched pathways unique to the IBD-PD, including MAPK signaling, LPS/IL-1 mediated inhibition of RXR function, and NAD signaling. Fourteen final candidate IBD-PD genes were prioritized by biological relatedness methods. The biological importance scores estimated by protein-protein interaction networks and pathway and ontology enrichment analyses indicated the involvement of genes related to immunity, inflammation, and autophagy in IBD-PD. Additionally, PheWAS provided support for the associations of candidate genes with IBD and PD. CONCLUSIONS Our study confirms and uncovers new LRRK2 associations in IBD-PD. The identification of novel inflammation and autophagy-related genes supports and expands previous findings related to IBD-PD pathogenesis, and underscores the significance of therapeutic interventions for reducing systemic inflammation.
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Affiliation(s)
- Meltem Ece Kars
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yiming Wu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- College of Life Science, China West Normal University, Nan Chong, Si Chuan, 637009, China
| | - Peter D Stenson
- Institute of Medical Genetics, Cardiff University, Cardiff, CF14 4XN, UK
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, CF14 4XN, UK
| | - Johan Burisch
- Gastrounit, Medical Division, Copenhagen University Hospital - Amager and Hvidovre, Kettegård Alle 30, Hvidovre, Copenhagen, 2650, Denmark
- Copenhagen Center for Inflammatory Bowel Disease in Children, Adolescents and Adults, Copenhagen University Hospital - Amager and Hvidovre, Kettegård Alle 30, Hvidovre, Copenhagen, 2650, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen, 2200, Denmark
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Yuval Itan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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Karpagavalli M, Sivagurunathan S, Panda TS, Srikakulam N, Arora R, Dohadwala L, Tiwary BK, Sadras SR, Arunachalam JP, Pandi G, Chidambaram S. piRNAs in the human retina and retinal pigment epithelium reveal a potential role in intracellular trafficking and oxidative stress. Mol Omics 2024; 20:248-264. [PMID: 38314503 DOI: 10.1039/d3mo00122a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Long considered active only in the germline, the PIWI/piRNA pathway is now known to play a significant role in somatic cells, especially neurons. In this study, piRNAs were profiled in the human retina and retinal pigment epithelium (RPE). Furthermore, RNA immunoprecipitation with HIWI2 (PIWIL4) in ARPE19 cells yielded 261 piRNAs, and the expression of selective piRNAs in donor eyes was assessed by qRT-PCR. Intriguingly, computational analysis revealed complete and partial seed sequence similarity between piR-hsa-26131 and the sensory organ specific miR-183/96/182 cluster. Furthermore, the expression of retina-enriched piR-hsa-26131 was positively correlated with miR-182 in HIWI2-silenced Y79 cells. In addition, the lnc-ZNF169 sequence matched with two miRNAs of the let-7 family, and piRNAs, piR-hsa-11361 and piR-hsa-11360, which could modulate the regulatory network of retinal differentiation. Interestingly, we annotated four enriched motifs among the piRNAs and found that the piRNAs containing CACAATG and CTCATCAKYG motifs were snoRNA-derived piRNAs, which are significantly associated with developmental functions. However, piRNAs consisting of ACCACTANACCAC and AKCACGYTCSC motifs were mainly tRNA-derived fragments linked to stress response and sensory perception. Additionally, co-expression network analysis revealed cell cycle control, intracellular transport and stress response as the important biological functions regulated by piRNAs in the retina. Moreover, loss of piRNAs in HIWI2 knockdown ARPE19 confirmed altered expression of targets implicated in intracellular transport, circadian clock, and retinal degeneration. Moreover, piRNAs were dysregulated under oxidative stress conditions, indicating their potential role in retinal pathology. Therefore, we postulate that piRNAs, miRNAs, and lncRNAs might have a functional interplay during retinal development and functions to regulate retinal homeostasis.
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Affiliation(s)
| | - Suganya Sivagurunathan
- RS Mehta Jain Department of Biochemistry and Cell Biology, Vision Research Foundation, Chennai, India
| | - T Sayamsmruti Panda
- Department of Bioinformatics, Pondicherry University, Puducherry-605014, India
| | - Nagesh Srikakulam
- Laboratory of RNA Biology and Epigenomics, Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Reety Arora
- National Centre for Biological Sciences, TIFR, Bangalore, India
| | | | - Basant K Tiwary
- Department of Bioinformatics, Pondicherry University, Puducherry-605014, India
| | - Sudha Rani Sadras
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry-605014, India.
| | - Jayamuruga Pandian Arunachalam
- Central Inter-Disciplinary Research Facility, Sri Balaji Vidyapeeth (Deemed to be University), Pondicherry-607402, India
| | - Gopal Pandi
- Laboratory of RNA Biology and Epigenomics, Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Subbulakshmi Chidambaram
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry-605014, India.
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3
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Calise SJ, O’Neill AG, Burrell AL, Dickinson MS, Molfino J, Clarke C, Quispe J, Sokolov D, Buey RM, Kollman JM. Light-sensitive phosphorylation regulates retinal IMPDH1 activity and filament assembly. J Cell Biol 2024; 223:e202310139. [PMID: 38323936 PMCID: PMC10849882 DOI: 10.1083/jcb.202310139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/11/2024] [Accepted: 01/23/2024] [Indexed: 02/08/2024] Open
Abstract
Inosine monophosphate dehydrogenase (IMPDH) is the rate-limiting enzyme in guanosine triphosphate (GTP) synthesis and assembles into filaments in cells, which desensitizes the enzyme to feedback inhibition and boosts nucleotide production. The vertebrate retina expresses two splice variants IMPDH1(546) and IMPDH1(595). In bovine retinas, residue S477 is preferentially phosphorylated in the dark, but the effects on IMPDH1 activity and regulation are unclear. Here, we generated phosphomimetic mutants to investigate structural and functional consequences of S477 phosphorylation. The S477D mutation resensitized both variants to GTP inhibition but only blocked assembly of IMPDH1(595) filaments. Cryo-EM structures of both variants showed that S477D specifically blocks assembly of a high-activity assembly interface, still allowing assembly of low-activity IMPDH1(546) filaments. Finally, we discovered that S477D exerts a dominant-negative effect in cells, preventing endogenous IMPDH filament assembly. By modulating the structure and higher-order assembly of IMPDH, S477 phosphorylation acts as a mechanism for downregulating retinal GTP synthesis in the dark when nucleotide turnover is decreased.
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Affiliation(s)
- S. John Calise
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Audrey G. O’Neill
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Anika L. Burrell
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Josephine Molfino
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Charlie Clarke
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - David Sokolov
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rubén M. Buey
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Justin M. Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
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4
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Yalaz C, Bridges E, Alham NK, Zois CE, Chen J, Bensaad K, Miar A, Pires E, Muschel RJ, McCullagh JSO, Harris AL. Cone photoreceptor phosphodiesterase PDE6H inhibition regulates cancer cell growth and metabolism, replicating the dark retina response. Cancer Metab 2024; 12:5. [PMID: 38350962 PMCID: PMC10863171 DOI: 10.1186/s40170-023-00326-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/24/2023] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND PDE6H encodes PDE6γ', the inhibitory subunit of the cGMP-specific phosphodiesterase 6 in cone photoreceptors. Inhibition of PDE6, which has been widely studied for its role in light transduction, increases cGMP levels. The purpose of this study is to characterise the role of PDE6H in cancer cell growth. METHODS From an siRNA screen for 487 genes involved in metabolism, PDE6H was identified as a controller of cell cycle progression in HCT116 cells. Role of PDE6H in cancer cell growth and metabolism was studied through the effects of its depletion on levels of cell cycle controllers, mTOR effectors, metabolite levels, and metabolic energy assays. Effect of PDE6H deletion on tumour growth was also studied in a xenograft model. RESULTS PDE6H knockout resulted in an increase of intracellular cGMP levels, as well as changes to the levels of nucleotides and key energy metabolism intermediates. PDE6H knockdown induced G1 cell cycle arrest and cell death and reduced mTORC1 signalling in cancer cell lines. Both knockdown and knockout of PDE6H resulted in the suppression of mitochondrial function. HCT116 xenografts revealed that PDE6H deletion, as well as treatment with the PDE5/6 inhibitor sildenafil, slowed down tumour growth and improved survival, while sildenafil treatment did not have an additive effect on slowing the growth of PDE6γ'-deficient tumours. CONCLUSIONS Our results indicate that the changes in cGMP and purine pools, as well as mitochondrial function which is observed upon PDE6γ' depletion, are independent of the PKG pathway. We show that in HCT116, PDE6H deletion replicates many effects of the dark retina response and identify PDE6H as a new target in preventing cancer cell proliferation and tumour growth.
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Affiliation(s)
- Ceren Yalaz
- Molecular Oncology Laboratories, Department of Medical Oncology, John Radcliffe Hospital, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.
| | - Esther Bridges
- Molecular Oncology Laboratories, Department of Medical Oncology, John Radcliffe Hospital, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Nasullah K Alham
- Department of Engineering Science, Institute of Biomedical Engineering (IBME), University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Christos E Zois
- Molecular Oncology Laboratories, Department of Medical Oncology, John Radcliffe Hospital, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Jianzhou Chen
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Karim Bensaad
- Molecular Oncology Laboratories, Department of Medical Oncology, John Radcliffe Hospital, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Ana Miar
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Elisabete Pires
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Ruth J Muschel
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - James S O McCullagh
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Adrian L Harris
- Molecular Oncology Laboratories, Department of Medical Oncology, John Radcliffe Hospital, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
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5
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Woulfe J, Munoz DG, Gray DA, Jinnah HA, Ivanova A. Inosine monophosphate dehydrogenase intranuclear inclusions are markers of aging and neuronal stress in the human substantia nigra. Neurobiol Aging 2024; 134:43-56. [PMID: 37992544 DOI: 10.1016/j.neurobiolaging.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023]
Abstract
We explored mechanisms involved in the age-dependent degeneration of human substantia nigra (SN) dopamine (DA) neurons. Owing to its important metabolic functions in post-mitotic neurons, we investigated the developmental and age-associated changes in the purine biosynthetic enzyme inosine monophosphate dehydrogenase (IMPDH). Tissue microarrays prepared from post-mortem samples of SN from 85 neurologically intact participants humans spanning the age spectrum were immunostained for IMPDH combined with other proteins. SN DA neurons contained two types of IMPDH structures: cytoplasmic IMPDH filaments and intranuclear IMPDH inclusions. The former were not age-restricted and may represent functional units involved in sustaining purine nucleotide supply in these highly metabolically active cells. The latter showed age-associated changes, including crystallization, features reminiscent of pathological inclusion bodies, and spatial associations with Marinesco bodies; structures previously associated with SN neuron dysfunction and death. We postulate dichotomous roles for these two subcellularly distinct IMPDH structures and propose a nucleus-based model for a novel mechanism of SN senescence that is independent of previously known neurodegeneration-associated proteins.
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Affiliation(s)
- John Woulfe
- Neuroscience Program, The Ottawa Hospital Research Institute, Ottawa, Ontario, Canada; Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada.
| | - David G Munoz
- Li Ka Shing Knowledge Institute & Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine, St. Michael's Hospital, Unity Health, University of Toronto, Toronto, Ontario, Canada
| | - Douglas A Gray
- Center for Cancer Therapeutics, The Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Hyder A Jinnah
- Departments of Neurology, Human Genetics & Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Alyona Ivanova
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children and Neurosurgery Research Department, St. Michael's Hospital, Toronto Unity Health, Toronto, Ontario, Canada
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6
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Lee TJ, Sasaki Y, Ruzycki PA, Ban N, Lin JB, Wu HT, Santeford A, Apte RS. Catalytic isoforms of AMP-activated protein kinase differentially regulate IMPDH activity and photoreceptor neuron function. JCI Insight 2024; 9:e173707. [PMID: 38227383 PMCID: PMC11143937 DOI: 10.1172/jci.insight.173707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 01/10/2024] [Indexed: 01/17/2024] Open
Abstract
AMP-activated protein kinase (AMPK) plays a crucial role in maintaining ATP homeostasis in photoreceptor neurons. AMPK is a heterotrimeric protein consisting of α, β, and γ subunits. The independent functions of the 2 isoforms of the catalytic α subunit, PRKAA1 and PRKAA2, are uncharacterized in specialized neurons, such as photoreceptors. Here, we demonstrate in mice that rod photoreceptors lacking PRKAA2, but not PRKAA1, showed altered levels of cGMP, GTP, and ATP, suggesting isoform-specific regulation of photoreceptor metabolism. Furthermore, PRKAA2-deficient mice displayed visual functional deficits on electroretinography and photoreceptor outer segment structural abnormalities on transmission electron microscopy consistent with neuronal dysfunction, but not neurodegeneration. Phosphoproteomics identified inosine monophosphate dehydrogenase (IMPDH) as a molecular driver of PRKAA2-specific photoreceptor dysfunction, and inhibition of IMPDH improved visual function in Prkaa2 rod photoreceptor-knockout mice. These findings highlight a therapeutically targetable PRKAA2 isoform-specific function of AMPK in regulating photoreceptor metabolism and function through a potentially previously uncharacterized mechanism affecting IMPDH activity.
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Affiliation(s)
- Tae Jun Lee
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences
- Department of Developmental Biology; and
| | - Yo Sasaki
- Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Philip A. Ruzycki
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences
- Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Norimitsu Ban
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Joseph B. Lin
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences
| | | | - Andrea Santeford
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences
| | - Rajendra S. Apte
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences
- Department of Developmental Biology; and
- Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
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7
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Sakti DH, Cornish EE, Nash BM, Jamieson RV, Grigg JR. IMPDH1-associated autosomal dominant retinitis pigmentosa: natural history of novel variant Lys314Gln and a comprehensive literature search. Ophthalmic Genet 2023; 44:437-455. [PMID: 37259572 DOI: 10.1080/13816810.2023.2215310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/11/2023] [Accepted: 05/14/2023] [Indexed: 06/02/2023]
Abstract
BACKGROUND Inosine monophosphate dehydrogenase (IMPDH) is a key regulatory enzyme in the de novo synthesis of the purine base guanine. Mutations in the inosine monophosphate dehydrogenase 1 gene (IMPDH1) are causative for RP10 autosomal dominant retinitis pigmentosa (adRP). This study reports a novel variant in a family with IMPDH1-associated retinopathy. We also performed a comprehensive review of all reported IMPDH1 disease causing variants with their associated phenotype. MATERIALS AND METHODS Multimodal imaging and functional studies documented the phenotype including best-corrected visual acuity (BCVA), fundus photograph, fundus autofluorescence (FAF), full field electroretinogram (ffERG), optical coherence tomography (OCT) and visual field (VF) data were collected. A literature search was performed in the PubMed and LOVD repositories. RESULTS We report 3 cases from a 2-generation family with a novel heterozygous likely pathogenic variant p. (Lys314Gln) (exon 10). The ophthalmic phenotype showed diffuse outer retinal atrophy with mild pigmentary changes with sparse pigmentary changes. FAF showed early macular involvement with macular hyperautofluorescence (hyperAF) surrounded by hypoAF. Foveal ellipsoid zone island can be found in the youngest patient but not in the older ones. The literature review identified a further 56 heterozygous, 1 compound heterozygous, and 2 homozygous variant. The heterozygous group included 43 missense, 3 in-frame, 1 nonsense, 2 frameshift, 1 synonymous, and 6 intronic variants. Exon 10 was noted as a hotspot harboring 18 variants. CONCLUSIONS We report a novel IMPDH1 variant. IMPDH1-associated retinopathy presents most frequently in the first decade of life with early macular involvement.
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Affiliation(s)
- Dhimas H Sakti
- Save Sight Institute, University of Sydney, Sydney, New South Wales, Australia
- Department of Ophthalmology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Elisa E Cornish
- Save Sight Institute, University of Sydney, Sydney, New South Wales, Australia
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Benjamin M Nash
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Sydney Children's Hospitals Network, Sydney, New South Wales, Australia
| | - Robyn V Jamieson
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - John R Grigg
- Save Sight Institute, University of Sydney, Sydney, New South Wales, Australia
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
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8
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Calise SJ, O’Neill AG, Burrell AL, Dickinson MS, Molfino J, Clarke C, Quispe J, Sokolov D, Buey RM, Kollman JM. Light-sensitive phosphorylation regulates enzyme activity and filament assembly of human IMPDH1 retinal splice variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558867. [PMID: 37790411 PMCID: PMC10542554 DOI: 10.1101/2023.09.21.558867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Inosine monophosphate dehydrogenase (IMPDH) is the rate-limiting enzyme in de novo guanosine triphosphate (GTP) synthesis and is controlled by feedback inhibition and allosteric regulation. IMPDH assembles into micron-scale filaments in cells, which desensitizes the enzyme to feedback inhibition by GTP and boosts nucleotide production. The vertebrate retina expresses two tissue-specific splice variants IMPDH1(546) and IMPDH1(595). IMPDH1(546) filaments adopt high and low activity conformations, while IMPDH1(595) filaments maintain high activity. In bovine retinas, residue S477 is preferentially phosphorylated in the dark, but the effects on IMPDH1 activity and regulation are unclear. Here, we generated phosphomimetic mutants to investigate structural and functional consequences of phosphorylation in IMPDH1 variants. The S477D mutation re-sensitized both variants to GTP inhibition, but only blocked assembly of IMPDH1(595) filaments and not IMPDH1(546) filaments. Cryo-EM structures of both variants showed that S477D specifically blocks assembly of the high activity assembly interface, still allowing assembly of low activity IMPDH1(546) filaments. Finally, we discovered that S477D exerts a dominant-negative effect in cells, preventing endogenous IMPDH filament assembly. By modulating the structure and higher-order assembly of IMPDH, phosphorylation at S477 acts as a mechanism for downregulating retinal GTP synthesis in the dark, when nucleotide turnover is decreased. Like IMPDH1, many other metabolic enzymes dynamically assemble filamentous polymers that allosterically regulate activity. Our work suggests that posttranslational modifications may be yet another layer of regulatory control to finely tune activity by modulating filament assembly in response to changing metabolic demands.
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Affiliation(s)
- S. John Calise
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Audrey G. O’Neill
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Anika L. Burrell
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Josephine Molfino
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Charlie Clarke
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - David Sokolov
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rubén M. Buey
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Justin M. Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
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9
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Keppeke GD, Chang CC, Zhang Z, Liu JL. Effect on cell survival and cytoophidium assembly of the adRP-10-related IMPDH1 missense mutation Asp226Asn. Front Cell Dev Biol 2023; 11:1234592. [PMID: 37731818 PMCID: PMC10507268 DOI: 10.3389/fcell.2023.1234592] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/17/2023] [Indexed: 09/22/2023] Open
Abstract
Introduction: Inosine monophosphate dehydrogenase 1 (IMPDH1) is a critical enzyme in the retina, essential for the correct functioning of photoreceptor cells. Mutations in IMPDH1 have been linked to autosomal dominant retinitis pigmentosa subtype 10 (adRP-10), a genetic eye disorder. Some of these mutations such as the Asp226Asn (D226N) lead to the assembly of large filamentous structures termed cytoophidia. D226N also gives IMPDH1 resistance to feedback inhibition by GDP/GTP. This study aims to emulate the adRP-10 condition with a long-term expression of IMPDH1-D226N in vitro and explore cytoophidium assembly and cell survival. We also assessed whether the introduction of an additional mutation (Y12C) to disrupt the cytoophidium has an attenuating effect on the toxicity caused by the D226N mutation. Results: Expression of IMPDH1-D226N in HEp-2 cells resulted in cytoophidium assembly in ∼70% of the cells, but the presence of the Y12C mutation disrupted the filaments. Long-term cell survival was significantly affected by the presence of the D226N mutation, with a decrease of ∼40% in the cells expressing IMPDH1-D226N when compared to IMPDH1-WT; however, survival was significantly recovered in IMPDH1-Y12C/D226N, with only a ∼10% decrease when compared to IMPDH1-WT. On the other hand, the IMPDH1 expression level in the D226N-positive cells was <30% of that of the IMPDH1-WT-positive cells and only slightly higher in the Y12C/D226N, suggesting that although cell survival in Y12C/D226N was recovered, higher expression levels of the mutated IMPDH1 were not tolerated by the cells in the long term. Conclusion: The IMPDH1-D226N effect on photoreceptor cell survival may be the result of a sum of problems: nucleotide unbalance plus a toxic long-life cytoophidium, supported by the observation that by introducing Y12C in IMPDH1 the cytoophidium was disrupted and cell survival significantly recovered, but not the sensibility to GDP/GTP regulation since higher expression levels of IMPDH1-D226N were not tolerated.
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Affiliation(s)
- Gerson Dierley Keppeke
- Departamento de Ciencias Biomédicas, Facultad de Medicina, Universidad Católica del Norte, Coquimbo, Chile
- Rheumatology Division, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, Brazil
| | - Chia-Chun Chang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Ziheng Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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10
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Daich Varela M, Georgiadis A, Michaelides M. Genetic treatment for autosomal dominant inherited retinal dystrophies: approaches, challenges and targeted genotypes. Br J Ophthalmol 2023; 107:1223-1230. [PMID: 36038193 DOI: 10.1136/bjo-2022-321903] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/01/2022] [Indexed: 11/04/2022]
Abstract
Inherited retinal diseases (IRDs) have been in the front line of gene therapy development for the last decade, providing a useful platform to test novel therapeutic approaches. More than 40 clinical trials have been completed or are ongoing, tackling autosomal recessive and X-linked conditions, mostly through adeno-associated viral vector delivery of a normal copy of the disease-causing gene. However, only recently has autosomal dominant (ad) disease been targeted, with the commencement of a trial for rhodopsin (RHO)-associated retinitis pigmentosa (RP), implementing antisense oligonucleotide (AON) therapy, with promising preliminary results (NCT04123626).Autosomal dominant RP represents 15%-25% of all RP, with RHO accounting for 20%-30% of these cases. Autosomal dominant macular and cone-rod dystrophies (MD/CORD) correspond to approximately 7.5% of all IRDs, and approximately 35% of all MD/CORD cases, with the main causative gene being BEST1 Autosomal dominant IRDs are not only less frequent than recessive, but also tend to be less severe and have later onset; for example, an individual with RHO-adRP would typically become severely visually impaired at an age 2-3 times older than in X-linked RPGR-RP.Gain-of-function and dominant negative aetiologies are frequently seen in the prevalent adRP genes RHO, RP1 and PRPF31 among others, which would not be effectively addressed by gene supplementation alone and need creative, novel approaches. Zinc fingers, RNA interference, AON, translational read-through therapy, and gene editing by clustered regularly interspaced short palindromic repeats/Cas are some of the strategies that are currently under investigation and will be discussed here.
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Affiliation(s)
- Malena Daich Varela
- Moorfields Eye Hospital, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | | | - Michel Michaelides
- Moorfields Eye Hospital, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
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11
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Camici M, Garcia-Gil M, Allegrini S, Pesi R, Bernardini G, Micheli V, Tozzi MG. Inborn Errors of Purine Salvage and Catabolism. Metabolites 2023; 13:787. [PMID: 37512494 PMCID: PMC10383617 DOI: 10.3390/metabo13070787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Cellular purine nucleotides derive mainly from de novo synthesis or nucleic acid turnover and, only marginally, from dietary intake. They are subjected to catabolism, eventually forming uric acid in humans, while bases and nucleosides may be converted back to nucleotides through the salvage pathways. Inborn errors of the purine salvage pathway and catabolism have been described by several researchers and are usually referred to as rare diseases. Since purine compounds play a fundamental role, it is not surprising that their dysmetabolism is accompanied by devastating symptoms. Nevertheless, some of these manifestations are unexpected and, so far, have no explanation or therapy. Herein, we describe several known inborn errors of purine metabolism, highlighting their unexplained pathological aspects. Our intent is to offer new points of view on this topic and suggest diagnostic tools that may possibly indicate to clinicians that the inborn errors of purine metabolism may not be very rare diseases after all.
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Affiliation(s)
- Marcella Camici
- Unità di Biochimica, Dipartimento di Biologia, Università di Pisa, Via San Zeno 51, 56127 Pisa, Italy
| | - Mercedes Garcia-Gil
- Unità di Fisiologia Generale, Dipartimento di Biologia, Università di Pisa, Via San Zeno 31, 56127 Pisa, Italy
- CISUP, Centro per l'Integrazione Della Strumentazione Dell'Università di Pisa, 56127 Pisa, Italy
- Centro di Ricerca Interdipartimentale Nutrafood "Nutraceuticals and Food for Health", Università di Pisa, 56126 Pisa, Italy
| | - Simone Allegrini
- Unità di Biochimica, Dipartimento di Biologia, Università di Pisa, Via San Zeno 51, 56127 Pisa, Italy
- CISUP, Centro per l'Integrazione Della Strumentazione Dell'Università di Pisa, 56127 Pisa, Italy
- Centro di Ricerca Interdipartimentale Nutrafood "Nutraceuticals and Food for Health", Università di Pisa, 56126 Pisa, Italy
| | - Rossana Pesi
- Unità di Biochimica, Dipartimento di Biologia, Università di Pisa, Via San Zeno 51, 56127 Pisa, Italy
| | - Giulia Bernardini
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Vanna Micheli
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
- LND Famiglie Italiane ODV-Via Giovanetti 15-20, 16149 Genova, Italy
| | - Maria Grazia Tozzi
- Unità di Biochimica, Dipartimento di Biologia, Università di Pisa, Via San Zeno 51, 56127 Pisa, Italy
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12
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Buey RM, Fernández‐Justel D, Jiménez A, Revuelta JL. The gateway to guanine nucleotides: Allosteric regulation of IMP dehydrogenases. Protein Sci 2022; 31:e4399. [PMID: 36040265 PMCID: PMC9375230 DOI: 10.1002/pro.4399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/07/2022] [Accepted: 07/19/2022] [Indexed: 11/12/2022]
Abstract
Inosine 5′‐monophosphate dehydrogenase (IMPDH) is an evolutionarily conserved enzyme that mediates the first committed step in de novo guanine nucleotide biosynthetic pathway. It is an essential enzyme in purine nucleotide biosynthesis that modulates the metabolic flux at the branch point between adenine and guanine nucleotides. IMPDH plays key roles in cell homeostasis, proliferation, and the immune response, and is the cellular target of several drugs that are widely used for antiviral and immunosuppressive chemotherapy. IMPDH enzyme is tightly regulated at multiple levels, from transcriptional control to allosteric modulation, enzyme filamentation, and posttranslational modifications. Herein, we review recent developments in our understanding of the mechanisms of IMPDH regulation, including all layers of allosteric control that fine‐tune the enzyme activity.
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Affiliation(s)
- Rubén M. Buey
- Metabolic Engineering Group, Department of Microbiology and Genetics Universidad de Salamanca Salamanca Spain
| | - David Fernández‐Justel
- Metabolic Engineering Group, Department of Microbiology and Genetics Universidad de Salamanca Salamanca Spain
| | - Alberto Jiménez
- Metabolic Engineering Group, Department of Microbiology and Genetics Universidad de Salamanca Salamanca Spain
| | - José L. Revuelta
- Metabolic Engineering Group, Department of Microbiology and Genetics Universidad de Salamanca Salamanca Spain
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13
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Zhu S, Huang J, Xu R, Wang Y, Wan Y, McNeel R, Parker E, Kolson D, Yam M, Webb B, Zhao C, Sigado J, Du J. Isocitrate dehydrogenase 3b is required for spermiogenesis but dispensable for retinal viability. J Biol Chem 2022; 298:102387. [PMID: 35985423 PMCID: PMC9478456 DOI: 10.1016/j.jbc.2022.102387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 12/02/2022] Open
Abstract
Isocitrate dehydrogenase 3 (IDH3) is a key enzyme in the mitochondrial tricarboxylic acid (TCA) cycle, which catalyzes the decarboxylation of isocitrate into α-ketoglutarate and concurrently converts NAD+ into NADH. Dysfunction of IDH3B, the β subunit of IDH3, has been previously correlated with retinal degeneration and male infertility in humans, but tissue-specific effects of IDH3 dysfunction are unclear. Here, we generated Idh3b-KO mice and found that IDH3B is essential for IDH3 activity in multiple tissues. We determined that loss of Idh3b in mice causes substantial accumulation of isocitrate and its precursors in the TCA cycle, particularly in the testes, whereas the levels of the downstream metabolites remain unchanged or slightly increased. However, the Idh3b-KO mice did not fully recapitulate the defects observed in humans. Global deletion of Idh3b only causes male infertility but not retinal degeneration in mice. Our investigation showed that loss of Idh3b causes an energetic deficit and disrupts the biogenesis of acrosome and flagellum, resulting in spermiogenesis arrestment in sperm cells. Together, we demonstrate that IDH3B controls its substrate levels in the TCA cycle, and it is required for sperm mitochondrial metabolism and spermiogenesis, highlighting the importance of the tissue-specific function of the ubiquitous TCA cycle.
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Affiliation(s)
- Siyan Zhu
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, WV 26506; Department of Biochemistry, West Virginia University, Morgantown, WV 26506; Department of Pharmaceutical and Pharmacological Science, West Virginia University, Morgantown, WV 26506
| | - Jiancheng Huang
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, WV 26506; Department of Biochemistry, West Virginia University, Morgantown, WV 26506; Eye Institute, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China; NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, and Shanghai Key Laboratory of Visual Impairment and Restoration (Fudan University), Shanghai, China
| | - Rong Xu
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, WV 26506; Department of Biochemistry, West Virginia University, Morgantown, WV 26506
| | - Yekai Wang
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, WV 26506; Department of Biochemistry, West Virginia University, Morgantown, WV 26506
| | - Yiming Wan
- Department of Biomedical Engineering Department, Stony Brook University, Stony Brook, NY 11794
| | - Rachel McNeel
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, WV 26506; Department of Biochemistry, West Virginia University, Morgantown, WV 26506
| | - Edward Parker
- Department of Ophthalmology, University of Washington, Seattle, WA 98109
| | - Douglas Kolson
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, WV 26506
| | - Michelle Yam
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, WV 26506; Department of Biochemistry, West Virginia University, Morgantown, WV 26506
| | - Bradley Webb
- Department of Biochemistry, West Virginia University, Morgantown, WV 26506
| | - Chen Zhao
- Eye Institute, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China; NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, and Shanghai Key Laboratory of Visual Impairment and Restoration (Fudan University), Shanghai, China
| | - Jenna Sigado
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, WV 26506; Department of Biochemistry, West Virginia University, Morgantown, WV 26506
| | - Jianhai Du
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, WV 26506; Department of Biochemistry, West Virginia University, Morgantown, WV 26506.
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14
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Fernández-Justel D, Marcos-Alcalde Í, Abascal F, Vidaña N, Gómez-Puertas P, Jiménez A, Revuelta JL, Buey RM. Diversity of mechanisms to control bacterial GTP homeostasis by the mutually exclusive binding of adenine and guanine nucleotides to IMP dehydrogenase. Protein Sci 2022; 31:e4314. [PMID: 35481629 PMCID: PMC9462843 DOI: 10.1002/pro.4314] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/21/2022] [Accepted: 04/06/2022] [Indexed: 02/06/2023]
Abstract
IMP dehydrogenase(IMPDH) is an essential enzyme that catalyzes the rate‐limiting step in the guanine nucleotide pathway. In eukaryotic cells, GTP binding to the regulatory domain allosterically controls the activity of IMPDH by a mechanism that is fine‐tuned by post‐translational modifications and enzyme polymerization. Nonetheless, the mechanisms of regulation of IMPDH in bacterial cells remain unclear. Using biochemical, structural, and evolutionary analyses, we demonstrate that, in most bacterial phyla, (p)ppGpp compete with ATP to allosterically modulate IMPDH activity by binding to a, previously unrecognized, conserved high affinity pocket within the regulatory domain. This pocket was lost during the evolution of Proteobacteria, making their IMPDHs insensitive to these alarmones. Instead, most proteobacterial IMPDHs evolved to be directly modulated by the balance between ATP and GTP that compete for the same allosteric binding site. Altogether, we demonstrate that the activity of bacterial IMPDHs is allosterically modulated by a universally conserved nucleotide‐controlled conformational switch that has divergently evolved to adapt to the specific particularities of each organism. These results reconcile the reported data on the crosstalk between (p)ppGpp signaling and the guanine nucleotide biosynthetic pathway and reinforce the essential role of IMPDH allosteric regulation on bacterial GTP homeostasis. PDB Code(s): 7PJI and 7PMZ;
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Affiliation(s)
- David Fernández-Justel
- Metabolic Engineering Group, Department of Microbiology and Genetics, Universidad de Salamanca, Salamanca, Spain
| | - Íñigo Marcos-Alcalde
- Molecular Modeling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), Madrid, Spain.,Biosciences Research Institute, School of Experimental Sciences, Universidad Francisco de Vitoria, Madrid, Spain
| | | | - Nerea Vidaña
- Metabolic Engineering Group, Department of Microbiology and Genetics, Universidad de Salamanca, Salamanca, Spain
| | - Paulino Gómez-Puertas
- Molecular Modeling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), Madrid, Spain
| | - Alberto Jiménez
- Metabolic Engineering Group, Department of Microbiology and Genetics, Universidad de Salamanca, Salamanca, Spain
| | - José L Revuelta
- Metabolic Engineering Group, Department of Microbiology and Genetics, Universidad de Salamanca, Salamanca, Spain
| | - Rubén M Buey
- Metabolic Engineering Group, Department of Microbiology and Genetics, Universidad de Salamanca, Salamanca, Spain
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15
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IMPDH dysregulation in disease: a mini review. Biochem Soc Trans 2022; 50:71-82. [PMID: 35191957 PMCID: PMC9022972 DOI: 10.1042/bst20210446] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 12/20/2022]
Abstract
Inosine-5′-monophosphate dehydrogenase (IMPDH) is a highly conserved enzyme in purine metabolism that is tightly regulated on multiple levels. IMPDH has a critical role in purine biosynthesis, where it regulates flux at the branch point between adenine and guanine nucleotide synthesis, but it also has a role in transcription regulation and other moonlighting functions have been described. Vertebrates have two isoforms, IMPDH1 and IMPDH2, and point mutations in each are linked to human disease. Mutations in IMPDH2 in humans are associated with neurodevelopmental disease, but the effects of mutations at the enzyme level have not yet been characterized. Mutations in IMPDH1 lead to retinal degeneration in humans, and recent studies have characterized how they cause functional defects in regulation. IMPDH1 is expressed as two unique splice variants in the retina, a tissue with very high and specific demands for purine nucleotides. Recent studies have revealed functional differences among splice variants, demonstrating that retinal variants up-regulate guanine nucleotide synthesis by reducing sensitivity to feedback inhibition by downstream products. A better understanding of the role of IMPDH1 in the retina and the characterization of an animal disease model will be critical for determining the molecular mechanism of IMPDH1-associated blindness.
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16
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Burrell AL, Nie C, Said M, Simonet JC, Fernández-Justel D, Johnson MC, Quispe J, Buey RM, Peterson JR, Kollman JM. IMPDH1 retinal variants control filament architecture to tune allosteric regulation. Nat Struct Mol Biol 2022; 29:47-58. [PMID: 35013599 PMCID: PMC9044917 DOI: 10.1038/s41594-021-00706-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/23/2021] [Indexed: 01/06/2023]
Abstract
Inosine-5'-monophosphate dehydrogenase (IMPDH), a key regulatory enzyme in purine nucleotide biosynthesis, dynamically assembles filaments in response to changes in metabolic demand. Humans have two isoforms: IMPDH2 filaments reduce sensitivity to feedback inhibition, while IMPDH1 assembly remains uncharacterized. IMPDH1 plays a unique role in retinal metabolism, and point mutants cause blindness. Here, in a series of cryogenic-electron microscopy structures we show that human IMPDH1 assembles polymorphic filaments with different assembly interfaces in extended and compressed states. Retina-specific splice variants introduce structural elements that reduce sensitivity to GTP inhibition, including stabilization of the extended filament form. Finally, we show that IMPDH1 disease mutations fall into two classes: one disrupts GTP regulation and the other has no effect on GTP regulation or filament assembly. These findings provide a foundation for understanding the role of IMPDH1 in retinal function and disease and demonstrate the diverse mechanisms by which metabolic enzyme filaments are allosterically regulated.
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Affiliation(s)
- Anika L Burrell
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Chuankai Nie
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Meerit Said
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jacqueline C Simonet
- Cancer Epigenetics and Signaling Program, Fox Chase Cancer Center, Philadelphia, PA, USA
- Department of Biology, Arcadia University, Glenside, PA, USA
| | - David Fernández-Justel
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Matthew C Johnson
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Structural Biology, Genentech, South San Francisco, CA, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rubén M Buey
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Jeffrey R Peterson
- Cancer Epigenetics and Signaling Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
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17
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Cleghorn WM, Burrell AL, Giarmarco MM, Brock DC, Wang Y, Chambers ZS, Du J, Kollman JM, Brockerhoff SE. A highly conserved zebrafish IMPDH retinal isoform produces the majority of guanine and forms dynamic protein filaments in photoreceptor cells. J Biol Chem 2022; 298:101441. [PMID: 34813793 PMCID: PMC8688572 DOI: 10.1016/j.jbc.2021.101441] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/12/2021] [Accepted: 11/13/2021] [Indexed: 12/18/2022] Open
Abstract
Inosine monophosphate dehydrogenase (IMPDH) is a key regulatory enzyme in the de novo synthesis of the purine base guanine. Dominant mutations in human IMPDH1 cause photoreceptor degeneration for reasons that are unknown. Here, we sought to provide some foundational information on Impdh1a in the zebrafish retina. We found that in zebrafish, gene subfunctionalization due to ancestral duplication resulted in a predominant retinal variant expressed exclusively in rod and cone photoreceptors. This variant is structurally and functionally similar to the human IMPDH1 retinal variant and shares a reduced sensitivity to GTP-mediated inhibition. We also demonstrated that Impdh1a forms prominent protein filaments in vitro and in vivo in both rod and cone photoreceptor cell bodies, synapses, and to a lesser degree, in outer segments. These filaments changed length and cellular distribution throughout the day consistent with diurnal changes in both mRNA and protein levels. The loss of Impdh1a resulted in a substantial reduction of guanine levels, although cellular morphology and cGMP levels remained normal. Our findings demonstrate a significant role for IMPDH1 in photoreceptor guanine production and provide fundamental new information on the details of this protein in the zebrafish retina.
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Affiliation(s)
- Whitney M Cleghorn
- Department of Biochemistry, University of Washington, Seattle, Washington, USA; Department of Ophthalmology, University of Washington, Seattle, Washington, USA
| | - Anika L Burrell
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | | | - Daniel C Brock
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Yekai Wang
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, West Virginia, USA; Department of Biochemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Zachary S Chambers
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Jianhai Du
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, West Virginia, USA; Department of Biochemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Susan E Brockerhoff
- Department of Biochemistry, University of Washington, Seattle, Washington, USA; Department of Ophthalmology, University of Washington, Seattle, Washington, USA.
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18
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Yan J, Chen Y, Zhu Y, Paquet-Durand F. Programmed Non-Apoptotic Cell Death in Hereditary Retinal Degeneration: Crosstalk between cGMP-Dependent Pathways and PARthanatos? Int J Mol Sci 2021; 22:10567. [PMID: 34638907 PMCID: PMC8508647 DOI: 10.3390/ijms221910567] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 12/20/2022] Open
Abstract
Programmed cell death (PCD) is a highly regulated process that results in the orderly destruction of a cell. Many different forms of PCD may be distinguished, including apoptosis, PARthanatos, and cGMP-dependent cell death. Misregulation of PCD mechanisms may be the underlying cause of neurodegenerative diseases of the retina, including hereditary retinal degeneration (RD). RD relates to a group of diseases that affect photoreceptors and that are triggered by gene mutations that are often well known nowadays. Nevertheless, the cellular mechanisms of PCD triggered by disease-causing mutations are still poorly understood, and RD is mostly still untreatable. While investigations into the neurodegenerative mechanisms of RD have focused on apoptosis in the past two decades, recent evidence suggests a predominance of non-apoptotic processes as causative mechanisms. Research into these mechanisms carries the hope that the knowledge created can eventually be used to design targeted treatments to prevent photoreceptor loss. Hence, in this review, we summarize studies on PCD in RD, including on apoptosis, PARthanatos, and cGMP-dependent cell death. Then, we focus on a possible interplay between these mechanisms, covering cGMP-signaling targets, overactivation of poly(ADP-ribose)polymerase (PARP), energy depletion, Ca2+-permeable channels, and Ca2+-dependent proteases. Finally, an outlook is given into how specific features of cGMP-signaling and PARthanatos may be targeted by therapeutic interventions.
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Affiliation(s)
| | | | | | - François Paquet-Durand
- Cell Death Mechanism Group, Institute for Ophthalmic Research, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076 Tübingen, Germany; (J.Y.); (Y.C.); (Y.Z.)
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19
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Maurais AJ, Salinger AJ, Tobin M, Shaffer SA, Weerapana E, Thompson PR. A Streamlined Data Analysis Pipeline for the Identification of Sites of Citrullination. Biochemistry 2021; 60:2902-2914. [PMID: 34491035 DOI: 10.1021/acs.biochem.1c00369] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Citrullination is an enzyme-catalyzed post-translational modification (PTM) that is essential for a host of biological processes, including gene regulation, programmed cell death, and organ development. While this PTM is required for normal cellular functions, aberrant citrullination is a hallmark of autoimmune disorders as well as cancer. Although aberrant citrullination is linked to human pathology, the exact role of citrullination in disease remains poorly characterized, in part because of the challenges associated with identifying the specific arginine residues that are citrullinated. Tandem mass spectrometry is the most precise method for uncovering sites of citrullination; however, due to the small mass shift (+0.984 Da) that results from citrullination, current database search algorithms commonly misannotate spectra, leading to a high number of false-positive assignments. To address this challenge, we developed an automated workflow to rigorously and rapidly mine proteomic data to unambiguously identify the sites of citrullination from complex peptide mixtures. The crux of this streamlined workflow is the ionFinder software program, which classifies citrullination sites with high confidence on the basis of the presence of diagnostic fragment ions. These diagnostic ions include the neutral loss of isocyanic acid, which is a dissociative event that is unique to citrulline residues. Using the ionFinder program, we have mapped the sites of autocitrullination on purified protein arginine deiminases (PAD1-4) and mapped the global citrullinome in a PAD2-overexpressing cell line. The ionFinder algorithm is a highly versatile, user-friendly, and open-source program that is agnostic to the type of instrument and mode of fragmentation that are used.
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Affiliation(s)
- Aaron J Maurais
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Ari J Salinger
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, LRB 826, 364 Plantation Street, Worcester, Massachusetts 01605, United States.,Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Micaela Tobin
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, LRB 826, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Scott A Shaffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, LRB 826, 364 Plantation Street, Worcester, Massachusetts 01605, United States.,Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, Massachusetts 01545, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Paul R Thompson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, LRB 826, 364 Plantation Street, Worcester, Massachusetts 01605, United States
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20
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Abstract
The outer retina is nourished from the choroid, a capillary bed just inside the sclera. O2, glucose, and other nutrients diffuse out of the choroid and then filter through a monolayer of retinal pigment epithelium (RPE) cells to fuel the retina. Recent studies of energy metabolism have revealed striking differences between retinas and RPE cells in the ways that they extract energy from fuels. The purpose of this review is to suggest and evaluate the hypothesis that the retina and RPE have complementary metabolic roles that make them depend on each other for survival and for their abilities to perform essential and specialized functions. Expected final online publication date for the Annual Review of Vision Science, Volume 7 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- James B Hurley
- Departments of Biochemistry and Ophthalmology, University of Washington, Seattle, Washington 98115, USA;
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21
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Terminal Peptide Extensions Augment the Retinal IMPDH1 Catalytic Activity and Attenuate the ATP-induced Fibrillation Events. Cell Biochem Biophys 2021; 79:221-229. [PMID: 33733369 DOI: 10.1007/s12013-021-00973-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2021] [Indexed: 12/11/2022]
Abstract
Defects in inosine monophosphate dehydrogenase-1 (IMPDH1) lead to insufficient biosyntheses of purine nucleotides. In eyes, these defects are believed to cause retinitis pigmentosa (RP). Major retinal isoforms of IMPDH1 are structurally distinct from those in other tissues, by bearing terminal extensions. Using recombinant mouse IMPDH1 (mH1), we evaluated the kinetics and oligomerization states of the retinal isoforms. Moreover, we adopted molecular simulation tools to study the possible effect of terminal tails on the function of major enzyme isoforms with the aim to find structural evidence in favor of contradictory observations on retinal IMPDH1 function. Our findings indicated higher catalytic activity for the major mouse retinal isoform (mH1603) along with lower fibrillation capacity under the influence of ATP. However, higher mass oligomerization products were formed by the mH1 (603) isoform in the presence of the enzyme inhibitors such as GTP and/or MPA. Collectively, our findings demonstrate that the structural differences between the retinal isoforms have led to functional variations possibly to justify the retinal cells' requirements.
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22
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Kofuji S, Sasaki AT. GTP metabolic reprogramming by IMPDH2: unlocking cancer cells' fuelling mechanism. J Biochem 2021; 168:319-328. [PMID: 32702086 DOI: 10.1093/jb/mvaa085] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/16/2020] [Indexed: 12/15/2022] Open
Abstract
Growing cells increase multiple biosynthetic processes in response to the high metabolic demands needed to sustain proliferation. The even higher metabolic requirements in the setting of cancer provoke proportionately greater biosynthesis. Underappreciated key aspects of this increased metabolic demand are guanine nucleotides and adaptive mechanisms to regulate their concentration. Using the malignant brain tumour, glioblastoma, as a model, we have demonstrated that one of the rate-limiting enzymes for guanosine triphosphate (GTP) synthesis, inosine monophosphate dehydrogenase-2 (IMPDH2), is increased and IMPDH2 expression is necessary for the activation of de novo GTP biosynthesis. Moreover, increased IMPDH2 enhances RNA polymerase I and III transcription directly linking GTP metabolism to both anabolic capacity as well as nucleolar enlargement historically observed as associated with cancer. In this review, we will review in detail the basis of these new discoveries and, more generally, summarize the current knowledge on the role of GTP metabolism in cancer.
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Affiliation(s)
- Satoshi Kofuji
- Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Atsuo T Sasaki
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, 3125 Eden Ave., Cincinnati, OH 45267-0508, USA.,Department of Cancer Biology, University of Cincinnati College of Medicine, 3125 Eden Ave., OH 45267-0508, USA.,Department of Neurosurgery, Brain Tumor Center at UC Gardner Neuroscience Institute, 3113 Bellevue Ave, Cincinnati, OH 45267-0508, USA.,Institute for Advanced Biosciences, Keio University, Kakuganji 246-2, Mizukami, Tsuruoka City, Yamagata 997-0052, Japan
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23
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Georgiou M, Grewal PS, Narayan A, Alser M, Ali N, Fujinami K, Webster AR, Michaelides M. Sector Retinitis Pigmentosa: Extending the Molecular Genetics Basis and Elucidating the Natural History. Am J Ophthalmol 2021; 221:299-310. [PMID: 32795431 PMCID: PMC7772805 DOI: 10.1016/j.ajo.2020.08.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/29/2020] [Accepted: 08/03/2020] [Indexed: 01/21/2023]
Abstract
Purpose To determine the genetic background of sector retinitis pigmentosa (RP) natural history to better inform patient counseling. Design Retrospective case series. Methods Review of clinical notes, retinal imaging including color fundus photography (CFP), fundus autofluorescence (FAF), optical coherence tomography (OCT), electrophysiological assessment (ERG), and molecular genetic testing were performed in patients with sector RP from a single tertiary referral center. Main outcomes measured were demographic data, signs and symptoms, visual acuity, molecular genetics; and ERG, FAF, and OCT findings. Results Twenty-six molecularly confirmed patients from 23 different families were identified harboring likely disease-causing variants in 9 genes. The modes of inheritance were autosomal recessive (AR, n=6: USH1C, n=2; MYO7A, n=2; CDH3, n=1; EYS, n=1), X-linked (XL, n=4: PRPS1, n=1; RPGR, n=3), and autosomal dominant (AD, n=16: IMPDH1, n=3; RP1, n=3; RHO, n=10), with a mean age of disease onset of 38.5, 30.5, and 39.0 years old, respectively. Five of these genes have not previously been reported to cause sector RP (PRPS1, MYO7A, EYS, IMPDH1, and RP1). Inferior and nasal predilection was common across the different genotypes, and patients tended to maintain good central vision. Progression on serial FAF was observed in RPGR, MYO7A, CDH23, EYS, IMPDH1, RP1, and RHO-associated sector RP. Conclusions The genotypic spectrum of the disease is broader than previously reported. The longitudinal data provided will help to make accurate patient prognoses and counseling as well as inform patients' potential participation in the increasing numbers of trials of novel therapeutics and access to future treatments. This is the largest series and longitudinal study in sector retinitis pigmentosa. The genotypic spectrum of the disease is broader than previously reported. The longitudinal data provided more accurate patient prognosis and counseling. The study informed patients' potential participation in the increasing numbers of trials of novel therapeutics and access to future treatments.
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Affiliation(s)
- Michalis Georgiou
- Institute of Ophthalmology, University College London, London, United Kingdom; UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Parampal S Grewal
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Akshay Narayan
- Institute of Ophthalmology, University College London, London, United Kingdom
| | - Muath Alser
- Institute of Ophthalmology, University College London, London, United Kingdom
| | - Naser Ali
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Kaoru Fujinami
- Institute of Ophthalmology, University College London, London, United Kingdom; UCL Institute of Ophthalmology, University College London, London, United Kingdom; Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan; Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Andrew R Webster
- Institute of Ophthalmology, University College London, London, United Kingdom; UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Michel Michaelides
- Institute of Ophthalmology, University College London, London, United Kingdom; UCL Institute of Ophthalmology, University College London, London, United Kingdom.
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24
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Calise SJ, Chan EKL. Anti-rods/rings autoantibody and IMPDH filaments: an update after fifteen years of discovery. Autoimmun Rev 2020; 19:102643. [PMID: 32805424 DOI: 10.1016/j.autrev.2020.102643] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 03/27/2020] [Indexed: 02/07/2023]
Abstract
Autoantibodies to unknown subcellular rod and ring-shaped structures were first discovered in sera from hepatitis C patients in 2005. Early studies showed a strong association between these anti-rods/rings antibodies (anti-RR) and the standard of care interferon-α plus ribavirin combination therapy (IFN/RBV), suggesting that anti-RR are drug-induced autoantibodies. In the context of hepatitis C, anti-RR have been linked with relapse from or lack of response to IFN/RBV in some patient cohorts. However, examples of anti-RR in other diseases and healthy individuals have also been reported over the years, although anti-RR remains a rare autoantibody response in general. The advent of new direct-acting antiviral drugs for chronic hepatitis C and studies of anti-RR from different parts of the world are also beginning to change the perception of anti-RR. The nucleotide biosynthetic enzyme inosine monophosphate dehydrogenase (IMPDH) has been identified as the major autoantigen recognized by anti-RR. Coincidentally, the assembly of IMPDH into micron-scale rod and ring-shaped structures was discovered around the same time as anti-RR. Knowledge of the fundamental biological properties and cellular functions of these structures, referred to as "IMPDH filaments" by cell biologists, has advanced in parallel to anti-RR antibodies. Recent studies have revealed that IMPDH filament assembly is a mechanism to prevent feedback inhibition of IMPDH and is therefore important for the increased nucleotide production required in hyperproliferating cells, like activated T cells. Fifteen years later, we review the history and current knowledge in both the anti-RR autoantibody and IMPDH filament fields. TAKE-HOME MESSAGE: Anti-rods/rings are recognized as an example of a drug-induced autoantibody in hepatitis C patients treated with interferon and ribavirin, although new studies suggest anti-rods/rings may be detected in other contexts and may depend on unknown environmental or genetic factors in different populations. Recent data suggest that the assembly of IMPDH into rod and ring structures, the targets of anti-rods/rings autoantibody, is a mechanism for hyperproliferating cells, like activated T cells, to maintain increased guanine nucleotide levels to support rapid cell division.
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Affiliation(s)
- S John Calise
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424, USA.
| | - Edward K L Chan
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424, USA.
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25
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Bennett LD, Klein M, John FT, Radojevic B, Jones K, Birch DG. Disease Progression in Patients with Autosomal Dominant Retinitis Pigmentosa due to a Mutation in Inosine Monophosphate Dehydrogenase 1 (IMPDH1). Transl Vis Sci Technol 2020; 9:14. [PMID: 32821486 PMCID: PMC7401855 DOI: 10.1167/tvst.9.5.14] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/10/2020] [Indexed: 02/06/2023] Open
Abstract
Purpose Mutations in the inosine monophosphate dehydrogenase 1 (IMPDH1) gene are a common cause of inherited retinal degeneration (IRD). Due to species- and tissue-dependent expression of IMPDH1, there are no appropriate models of human IMPDH1 disease. Therefore, a limited understanding remains of disease expression and rates of progression for IMPDH1-related IRD. Methods We evaluated semiautomated kinetic and chromatic static perimetry, spectral-domain optical coherence tomography (SD-OCT), and ultra-wide field fundus images with autofluorescence in a cohort of 12 patients (ages 11–58 at first visit). Ten patients had longitudinal data for which rates of progression were estimated. Results Visual acuities were relatively stable over time and the photoreceptors within the central retina remained intact. Perifoveal photoreceptor loss measured over a period of years coincided with visual fields, which were constricted and progressed over time in all patients. Rod sensitivity showed a similar pattern of defect to that of the kinetic perimetry and the autofluorescence ultra-wide field imaging. Full-field electroretinograms were severely reduced and the dark-adapted rod and mixed responses were extinguished at earlier visits than the light-adapted cone responses. Conclusions There was variability in disease severity at the first visit, but results show that the peripheral retina is more susceptible to the deleterious consequences of an IMPDH1 mutation. Given the pattern of degeneration and the alternatively spliced isoforms of IMPDH1, potential interventions may consider targeting the periphery early in disease, modulating transcript expression, and/or preserving central vision at late stages of the disease. Translational Relevance These results inform clinical prognosis and offer evidence strategies toward therapeutic intervention.
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Affiliation(s)
- Lea D Bennett
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Martin Klein
- Retina Foundation of the Southwest, Dallas, TX, USA
| | - Finny T John
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Bojana Radojevic
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kaylie Jones
- Retina Foundation of the Southwest, Dallas, TX, USA
| | - David G Birch
- Retina Foundation of the Southwest, Dallas, TX, USA.,Department of Ophthalmology, UT Southwestern Medical Center, Dallas, TX, USA
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26
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Plana-Bonamaisó A, López-Begines S, Fernández-Justel D, Junza A, Soler-Tapia A, Andilla J, Loza-Alvarez P, Rosa JL, Miralles E, Casals I, Yanes O, de la Villa P, Buey RM, Méndez A. Post-translational regulation of retinal IMPDH1 in vivo to adjust GTP synthesis to illumination conditions. eLife 2020; 9:56418. [PMID: 32254022 PMCID: PMC7176436 DOI: 10.7554/elife.56418] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/30/2020] [Indexed: 02/06/2023] Open
Abstract
We report the in vivo regulation of Inosine-5´-monophosphate dehydrogenase 1 (IMPDH1) in the retina. IMPDH1 catalyzes the rate-limiting step in the de novo synthesis of guanine nucleotides, impacting the cellular pools of GMP, GDP and GTP. Guanine nucleotide homeostasis is central to photoreceptor cells, where cGMP is the signal transducing molecule in the light response. Mutations in IMPDH1 lead to inherited blindness. We unveil a light-dependent phosphorylation of retinal IMPDH1 at Thr159/Ser160 in the Bateman domain that desensitizes the enzyme to allosteric inhibition by GDP/GTP. When exposed to bright light, living mice increase the rate of GTP and ATP synthesis in their retinas; concomitant with IMPDH1 aggregate formation at the outer segment layer. Inhibiting IMPDH activity in living mice delays rod mass recovery. We unveil a novel mechanism of regulation of IMPDH1 in vivo, important for understanding GTP homeostasis in the retina and the pathogenesis of adRP10 IMPDH1 mutations.
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Affiliation(s)
- Anna Plana-Bonamaisó
- Department of Physiological Sciences, School of Medicine, Campus Universitari de Bellvitge, University of Barcelona, Barcelona, Spain.,Institut de Neurociències, Campus Universitari de Bellvitge, University of Barcelona, Barcelona, Spain
| | - Santiago López-Begines
- Department of Physiological Sciences, School of Medicine, Campus Universitari de Bellvitge, University of Barcelona, Barcelona, Spain
| | - David Fernández-Justel
- Metabolic Engineering Group, Department of Microbiology and Genetics. University of Salamanca, Salamanca, Spain
| | - Alexandra Junza
- CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), Madrid, Spain.,Metabolomics Platform, IISPV, Department of Electronic Engineering, Universitat Rovira i Virgili, Tarragona, Spain
| | - Ariadna Soler-Tapia
- Department of Physiological Sciences, School of Medicine, Campus Universitari de Bellvitge, University of Barcelona, Barcelona, Spain
| | - Jordi Andilla
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, Spain
| | - Pablo Loza-Alvarez
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, Spain
| | - Jose Luis Rosa
- Department of Physiological Sciences, School of Medicine, Campus Universitari de Bellvitge, University of Barcelona, Barcelona, Spain.,Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Campus Universitari de Bellvitge, University of Barcelona, Barcelona, Spain
| | - Esther Miralles
- Centres Cientifics i Tecnològics (CCiTUB), University of Barcelona, Parc Científic de Barcelona, Barcelona, Spain
| | - Isidre Casals
- Centres Cientifics i Tecnològics (CCiTUB), University of Barcelona, Parc Científic de Barcelona, Barcelona, Spain
| | - Oscar Yanes
- CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), Madrid, Spain.,Metabolomics Platform, IISPV, Department of Electronic Engineering, Universitat Rovira i Virgili, Tarragona, Spain
| | - Pedro de la Villa
- Physiology Unit, Dept of Systems Biology, School of Medicine, University of Alcalá, Madrid, Spain.,Visual Neurophysiology Group-IRYCIS, Madrid, Spain
| | - Ruben M Buey
- Metabolic Engineering Group, Department of Microbiology and Genetics. University of Salamanca, Salamanca, Spain
| | - Ana Méndez
- Department of Physiological Sciences, School of Medicine, Campus Universitari de Bellvitge, University of Barcelona, Barcelona, Spain.,Institut de Neurociències, Campus Universitari de Bellvitge, University of Barcelona, Barcelona, Spain.,Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Campus Universitari de Bellvitge, University of Barcelona, Barcelona, Spain
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27
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Johnson MC, Kollman JM. Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation. eLife 2020; 9:e53243. [PMID: 31999252 PMCID: PMC7018514 DOI: 10.7554/elife.53243] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/29/2020] [Indexed: 02/06/2023] Open
Abstract
Inosine monophosphate dehydrogenase (IMPDH) mediates the first committed step in guanine nucleotide biosynthesis and plays important roles in cellular proliferation and the immune response. IMPDH reversibly polymerizes in cells and tissues in response to changes in metabolic demand. Self-assembly of metabolic enzymes is increasingly recognized as a general mechanism for regulating activity, typically by stabilizing specific conformations of an enzyme, but the regulatory role of IMPDH filaments has remained unclear. Here, we report a series of human IMPDH2 cryo-EM structures in both active and inactive conformations. The structures define the mechanism of filament assembly, and reveal how filament-dependent allosteric regulation of IMPDH2 makes the enzyme less sensitive to feedback inhibition, explaining why assembly occurs under physiological conditions that require expansion of guanine nucleotide pools. Tuning sensitivity to an allosteric inhibitor distinguishes IMPDH from other metabolic filaments, and highlights the diversity of regulatory outcomes that can emerge from self-assembly.
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Affiliation(s)
- Matthew C Johnson
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
| | - Justin M Kollman
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
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28
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Power M, Das S, Schütze K, Marigo V, Ekström P, Paquet-Durand F. Cellular mechanisms of hereditary photoreceptor degeneration - Focus on cGMP. Prog Retin Eye Res 2019; 74:100772. [PMID: 31374251 DOI: 10.1016/j.preteyeres.2019.07.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 07/25/2019] [Accepted: 07/29/2019] [Indexed: 12/21/2022]
Abstract
The cellular mechanisms underlying hereditary photoreceptor degeneration are still poorly understood, a problem that is exacerbated by the enormous genetic heterogeneity of this disease group. However, the last decade has yielded a wealth of new knowledge on degenerative pathways and their diversity. Notably, a central role of cGMP-signalling has surfaced for photoreceptor cell death triggered by a subset of disease-causing mutations. In this review, we examine key aspects relevant for photoreceptor degeneration of hereditary origin. The topics covered include energy metabolism, epigenetics, protein quality control, as well as cGMP- and Ca2+-signalling, and how the related molecular and metabolic processes may trigger photoreceptor demise. We compare and integrate evidence on different cell death mechanisms that have been associated with photoreceptor degeneration, including apoptosis, necrosis, necroptosis, and PARthanatos. A special focus is then put on the mechanisms of cGMP-dependent cell death and how exceedingly high photoreceptor cGMP levels may cause activation of Ca2+-dependent calpain-type proteases, histone deacetylases and poly-ADP-ribose polymerase. An evaluation of the available literature reveals that a large group of patients suffering from hereditary photoreceptor degeneration carry mutations that are likely to trigger cGMP-dependent cell death, making this pathway a prime target for future therapy development. Finally, an outlook is given into technological and methodological developments that will with time likely contribute to a comprehensive overview over the entire metabolic complexity of photoreceptor cell death. Building on such developments, new imaging technology and novel biomarkers may be used to develop clinical test strategies, that fully consider the genetic heterogeneity of hereditary retinal degenerations, in order to facilitate clinical testing of novel treatment approaches.
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Affiliation(s)
- Michael Power
- Cell Death Mechanism Group, Institute for Ophthalmic Research, University of Tübingen, Germany; Centre for Integrative Neurosciences (CIN), University of Tübingen, Germany; Graduate Training Centre of Neuroscience (GTC), University of Tübingen, Germany
| | - Soumyaparna Das
- Cell Death Mechanism Group, Institute for Ophthalmic Research, University of Tübingen, Germany; Graduate Training Centre of Neuroscience (GTC), University of Tübingen, Germany
| | | | - Valeria Marigo
- Department of Life Sciences, University of Modena and Reggio Emilia, Italy
| | - Per Ekström
- Ophthalmology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Sweden
| | - François Paquet-Durand
- Cell Death Mechanism Group, Institute for Ophthalmic Research, University of Tübingen, Germany.
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29
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Garcia‐Seisdedos H, Villegas JA, Levy ED. Infinite Ansammlungen gefalteter Proteine im Kontext von Evolution, Krankheiten und Proteinentwicklung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201806092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - José A. Villegas
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
| | - Emmanuel D. Levy
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
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30
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Garcia-Seisdedos H, Villegas JA, Levy ED. Infinite Assembly of Folded Proteins in Evolution, Disease, and Engineering. Angew Chem Int Ed Engl 2019; 58:5514-5531. [PMID: 30133878 PMCID: PMC6471489 DOI: 10.1002/anie.201806092] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/06/2018] [Indexed: 12/14/2022]
Abstract
Mutations and changes in a protein's environment are well known for their potential to induce misfolding and aggregation, including amyloid formation. Alternatively, such perturbations can trigger new interactions that lead to the polymerization of folded proteins. In contrast to aggregation, this process does not require misfolding and, to highlight this difference, we refer to it as agglomeration. This term encompasses the amorphous assembly of folded proteins as well as the polymerization in one, two, or three dimensions. We stress the remarkable potential of symmetric homo‐oligomers to agglomerate even by single surface point mutations, and we review the double‐edged nature of this potential: how aberrant assemblies resulting from agglomeration can lead to disease, but also how agglomeration can serve in cellular adaptation and be exploited for the rational design of novel biomaterials.
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Affiliation(s)
| | - José A Villegas
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
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31
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Park KS, Xu CL, Cui X, Tsang SH. Reprogramming the metabolome rescues retinal degeneration. Cell Mol Life Sci 2018; 75:1559-1566. [PMID: 29332245 PMCID: PMC9377522 DOI: 10.1007/s00018-018-2744-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/27/2017] [Accepted: 01/02/2018] [Indexed: 02/03/2023]
Abstract
Metabolomics studies in the context of ophthalmology have largely focused on identifying metabolite concentrations that characterize specific retinal diseases. Studies involving mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy have shown that individuals suffering from retinal diseases exhibit metabolic profiles that markedly differ from those of control individuals, supporting the notion that metabolites may serve as easily identifiable biomarkers for specific conditions. An emerging branch of metabolomics resulting from biomarker studies, however, involves the study of retinal metabolic dysfunction as causes of degeneration. Recent publications have identified a number of metabolic processes-including but not limited to glucose and oxygen metabolism-that, when perturbed, play a role in the degeneration of photoreceptor cells. As a result, such studies have led to further research elucidating methods for prolonging photoreceptor survival in an effort to halt degeneration in its early stages. This review will explore the ways in which metabolomics has deepened our understanding of the causes of retinal degeneration and discuss how metabolomics can be used to prevent retinal degeneration from progressing to its later disease stages.
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Affiliation(s)
- Karen Sophia Park
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University, New York, NY, USA
- Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Christine L Xu
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University, New York, NY, USA
- Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Xuan Cui
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University, New York, NY, USA
- Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Stephen H Tsang
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University, New York, NY, USA.
- Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA.
- Departments of Ophthalmology, Pathology, and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, USA.
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32
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Pua KH, Stiles DT, Sowa ME, Verdine GL. IMPDH2 Is an Intracellular Target of the Cyclophilin A and Sanglifehrin A Complex. Cell Rep 2017; 18:432-442. [PMID: 28076787 DOI: 10.1016/j.celrep.2016.12.030] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/21/2016] [Accepted: 12/10/2016] [Indexed: 11/16/2022] Open
Abstract
Natural products have demonstrated utility in the clinic and can also act as probes to understand complex cellular pathways. Sanglifehrin A (SFA) is a mixed polyketide and non-ribosomal peptide synthase natural product with sub-nano-molar affinity for its receptor cyclophilin A (PPIA). It has been shown to behave in vitro as an immune suppressant. Here, we identify inosine-5'-monophosphate dehydrogenase 2 (IMPDH2) as an intracellular target of the PPIA-SFA binary complex. The formation of this ternary complex does not inhibit the enzymatic activity of IMPDH2. Rather, ternary complex formation modulates cell growth through interaction with the cystathionine-β-synthase (CBS) domain of IMPDH2. We further demonstrate that the SFA complex is highly isoform selective for IMPDH2 (versus IMPDH1). This work reveals a role for the CBS domains of IMPDH2 in cellular proliferation, suggesting a more complex role than previously suspected for IMPDH2 in T cell activation and proliferation.
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Affiliation(s)
- Khian Hong Pua
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Warp Drive Bio, Cambridge, MA 02139, USA
| | - Dylan T Stiles
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Warp Drive Bio, Cambridge, MA 02139, USA
| | - Mathew E Sowa
- Warp Drive Bio, Cambridge, MA 02139, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Gregory L Verdine
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Warp Drive Bio, Cambridge, MA 02139, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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33
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Campbell M, Cassidy PS, O'Callaghan J, Crosbie DE, Humphries P. Manipulating ocular endothelial tight junctions: Applications in treatment of retinal disease pathology and ocular hypertension. Prog Retin Eye Res 2017; 62:120-133. [PMID: 28951125 DOI: 10.1016/j.preteyeres.2017.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/01/2017] [Accepted: 09/20/2017] [Indexed: 11/25/2022]
Abstract
Protein levels of endothelial tight-junctions of the inner retinal microvasculature, together with those of Schlemm's canal, can be readily manipulated by RNA interference (RNAi), resulting in the paracellular clefts between such cells to be reversibly modulated. This facilitates access to the retina of systemically-deliverable low molecular weight, potentially therapeutic compounds, while also allowing potentially toxic material, for example, soluble Amyloid-β1-40, to be removed from the retina into the peripheral circulation. The technique has also been shown to be highly effective in alleviation of pathological cerebral oedema and we speculate that it may therefore have similar utility in the oedematous retina. Additionally, by manipulating endothelial tight-junctions of Schlemm's canal, inflow of aqueous humour from the trabecular meshwork into the Canal can be radically enhanced, suggesting a novel avenue for control of intraocular pressure. Here, we review the technology underlying this approach together with specific examples of clinical targets that are, or could be, amenable to this novel form of genetic intervention.
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Affiliation(s)
- Matthew Campbell
- Smurfit Institute of Genetics, Lincoln Place Gate, Trinity College Dublin, Dublin 2, Ireland.
| | - Paul S Cassidy
- Smurfit Institute of Genetics, Lincoln Place Gate, Trinity College Dublin, Dublin 2, Ireland
| | - Jeffrey O'Callaghan
- Smurfit Institute of Genetics, Lincoln Place Gate, Trinity College Dublin, Dublin 2, Ireland
| | - Darragh E Crosbie
- Smurfit Institute of Genetics, Lincoln Place Gate, Trinity College Dublin, Dublin 2, Ireland
| | - Pete Humphries
- Smurfit Institute of Genetics, Lincoln Place Gate, Trinity College Dublin, Dublin 2, Ireland.
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Yang H, Fang Z, Wei Y, Bohannan ZS, Gañán-Gómez I, Pierola AA, Paradiso LJ, Iwamura H, Garcia-Manero G. Preclinical activity of FF-10501-01, a novel inosine-5'-monophosphate dehydrogenase inhibitor, in acute myeloid leukemia. Leuk Res 2017; 59:85-92. [PMID: 28599189 DOI: 10.1016/j.leukres.2017.05.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/22/2017] [Accepted: 05/23/2017] [Indexed: 01/20/2023]
Abstract
BACKGROUND FF-10501-01 is a selective inosine monophosphate dehydrogenase (IMPDH) inhibitor that has shown activity in cancer cell lines. We studied whether FF-10501-01 is effective in targeting a variety of hypomethylating agent (HMA)-sensitive and -resistant acute myelogenous leukemia (AML) cell lines. METHODS We treated multiple cell lines (including HMA-resistant cells) with FF-10501-01 and analyzed proliferation, apoptosis, and cell cycle status. We also assessed HMA-FF-10501-01 combinations and the ability of extracellular guanosine to rescue cell proliferation in FF-10501-01-treated cells. We performed high-performance liquid chromatography (HPLC) to study guanine nucleotide levels in treated and untreated cells. Finally, we studied the effects of FF-10501-01 in fresh peripheral blood cells taken from AML patients. RESULTS FF-10501-01 showed a strong dose-dependent effect on proliferation and induced apoptosis at approximately 30μM. The effects of FF-10501-01 treatment on cell cycle status were variable, with no statistically significant trends. Guanosine rescued proliferation in FF-10501-01-treated cells, and HPLC results showed significant decreases in phosphorylated guanosine levels in MOLM13 cells. FF-10501-01 effectively reduced proliferation at concentrations of 300μM and above in 3 primary AML samples. CONCLUSIONS FF-10501-01 effectively induces AML cell death and reduces AML peripheral blood cell proliferation by targeting guanine nucleotide biosynthesis regardless of HMA resistance status.
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Affiliation(s)
- Hui Yang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Zhihong Fang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Yue Wei
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Zachary S Bohannan
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Irene Gañán-Gómez
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ana Alfonso Pierola
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | | | - Guillermo Garcia-Manero
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.
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Broadgate S, Yu J, Downes SM, Halford S. Unravelling the genetics of inherited retinal dystrophies: Past, present and future. Prog Retin Eye Res 2017; 59:53-96. [PMID: 28363849 DOI: 10.1016/j.preteyeres.2017.03.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 02/07/2023]
Abstract
The identification of the genes underlying monogenic diseases has been of interest to clinicians and scientists for many years. Using inherited retinal dystrophies as an example of monogenic disease we describe the history of molecular genetic techniques that have been pivotal in the discovery of disease causing genes. The methods that were developed in the 1970's and 80's are still in use today but have been refined and improved. These techniques enabled the concept of the Human Genome Project to be envisaged and ultimately realised. When the successful conclusion of the project was announced in 2003 many new tools and, as importantly, many collaborations had been developed that facilitated a rapid identification of disease genes. In the post-human genome project era advances in computing power and the clever use of the properties of DNA replication has allowed the development of next-generation sequencing technologies. These methods have revolutionised the identification of disease genes because for the first time there is no need to define the position of the gene in the genome. The use of next generation sequencing in a diagnostic setting has allowed many more patients with an inherited retinal dystrophy to obtain a molecular diagnosis for their disease. The identification of novel genes that have a role in the development or maintenance of retinal function is opening up avenues of research which will lead to the development of new pharmacological and gene therapy approaches. Neither of which can be used unless the defective gene and protein is known. The continued development of sequencing technologies also holds great promise for the advent of truly personalised medicine.
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Affiliation(s)
- Suzanne Broadgate
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Levels 5 and 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Jing Yu
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Levels 5 and 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Susan M Downes
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, Oxford, OX3 9DU, UK
| | - Stephanie Halford
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Levels 5 and 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK.
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Karali M, Persico M, Mutarelli M, Carissimo A, Pizzo M, Singh Marwah V, Ambrosio C, Pinelli M, Carrella D, Ferrari S, Ponzin D, Nigro V, di Bernardo D, Banfi S. High-resolution analysis of the human retina miRNome reveals isomiR variations and novel microRNAs. Nucleic Acids Res 2016; 44:1525-40. [PMID: 26819412 PMCID: PMC4770244 DOI: 10.1093/nar/gkw039] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 01/13/2016] [Indexed: 01/14/2023] Open
Abstract
MicroRNAs play a fundamental role in retinal development and function. To characterise the miRNome of the human retina, we carried out deep sequencing analysis on sixteen individuals. We established the catalogue of retina-expressed miRNAs, determined their relative abundance and found that a small number of miRNAs accounts for almost 90% of the retina miRNome. We discovered more than 3000 miRNA variants (isomiRs), encompassing a wide range of sequence variations, which include seed modifications that are predicted to have an impact on miRNA action. We demonstrated that a seed-modifying isomiR of the retina-enriched miR-124-3p was endowed with different targeting properties with respect to the corresponding canonical form. Moreover, we identified 51 putative novel, retina-specific miRNAs and experimentally validated the expression for nine of them. Finally, a parallel analysis of the human Retinal Pigment Epithelium (RPE)/choroid, two tissues that are known to be crucial for retina homeostasis, yielded notably distinct miRNA enrichment patterns compared to the retina. The generated data are accessible through an ad hoc database. This study is the first to reveal the complexity of the human retina miRNome at nucleotide resolution and constitutes a unique resource to assess the contribution of miRNAs to the pathophysiology of the human retina.
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Affiliation(s)
- Marianthi Karali
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, via Luigi De Crecchio 7, 80138 Naples (NA), Italy
| | - Maria Persico
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Margherita Mutarelli
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Annamaria Carissimo
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Mariateresa Pizzo
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Veer Singh Marwah
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Concetta Ambrosio
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Michele Pinelli
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Diego Carrella
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Stefano Ferrari
- Eye Bank of Venice, Padiglione Rama, via Paccagnella 11, 30174 Zelarino (VE), Italy
| | - Diego Ponzin
- Eye Bank of Venice, Padiglione Rama, via Paccagnella 11, 30174 Zelarino (VE), Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, via Luigi De Crecchio 7, 80138 Naples (NA), Italy
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy Department of Chemical, Materials and Production Engineering, University of Naples 'Federico II', via Claudio 21, 80125 Naples (NA), Italy
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, via Luigi De Crecchio 7, 80138 Naples (NA), Italy
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Guanine nucleotide binding to the Bateman domain mediates the allosteric inhibition of eukaryotic IMP dehydrogenases. Nat Commun 2015; 6:8923. [PMID: 26558346 PMCID: PMC4660370 DOI: 10.1038/ncomms9923] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 10/16/2015] [Indexed: 12/26/2022] Open
Abstract
Inosine-5′-monophosphate dehydrogenase (IMPDH) plays key roles in purine nucleotide metabolism and cell proliferation. Although IMPDH is a widely studied therapeutic target, there is limited information about its physiological regulation. Using Ashbya gossypii as a model, we describe the molecular mechanism and the structural basis for the allosteric regulation of IMPDH by guanine nucleotides. We report that GTP and GDP bind to the regulatory Bateman domain, inducing octamers with compromised catalytic activity. Our data suggest that eukaryotic and prokaryotic IMPDHs might have developed different regulatory mechanisms, with GTP/GDP inhibiting only eukaryotic IMPDHs. Interestingly, mutations associated with human retinopathies map into the guanine nucleotide-binding sites including a previously undescribed non-canonical site and disrupt allosteric inhibition. Together, our results shed light on the mechanisms of the allosteric regulation of enzymes mediated by Bateman domains and provide a molecular basis for certain retinopathies, opening the door to new therapeutic approaches. IMP dehydrogenase (IMPDH) plays essential roles in purine metabolism and cell proliferation. Here Buey et al. describe a guanine nucleotides regulated molecular mechanism for allosteric communication between the regulatory and catalytic domains of IMPDH.
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Lake JI, Avetisyan M, Zimmermann AG, Heuckeroth RO. Neural crest requires Impdh2 for development of the enteric nervous system, great vessels, and craniofacial skeleton. Dev Biol 2015; 409:152-165. [PMID: 26546974 DOI: 10.1016/j.ydbio.2015.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 11/02/2015] [Accepted: 11/03/2015] [Indexed: 10/22/2022]
Abstract
Mutations that impair the proliferation of enteric neural crest-derived cells (ENCDC) cause Hirschsprung disease, a potentially lethal birth defect where the enteric nervous system (ENS) is absent from distal bowel. Inosine 5' monophosphate dehydrogenase (IMPDH) activity is essential for de novo GMP synthesis, and chemical inhibition of IMPDH induces Hirschsprung disease-like pathology in mouse models by reducing ENCDC proliferation. Two IMPDH isoforms are ubiquitously expressed in the embryo, but only IMPDH2 is required for life. To further understand the role of IMPDH2 in ENS and neural crest development, we characterized a conditional Impdh2 mutant mouse. Deletion of Impdh2 in the early neural crest using the Wnt1-Cre transgene produced defects in multiple neural crest derivatives including highly penetrant intestinal aganglionosis, agenesis of the craniofacial skeleton, and cardiac outflow tract and great vessel malformations. Analysis using a Rosa26 reporter mouse suggested that some or all of the remaining ENS in Impdh2 conditional-knockout animals was derived from cells that escaped Wnt1-Cre mediated DNA recombination. These data suggest that IMPDH2 mediated guanine nucleotide synthesis is essential for normal development of the ENS and other neural crest derivatives.
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Affiliation(s)
- Jonathan I Lake
- Department of Pediatrics and Department of Developmental Regenerative and Stem Cell Biology, Washington University School of Medicine, 660 South Euclid Avenue, Box 8208, St. Louis, MO 63021, USA
| | - Marina Avetisyan
- Department of Pediatrics and Department of Developmental Regenerative and Stem Cell Biology, Washington University School of Medicine, 660 South Euclid Avenue, Box 8208, St. Louis, MO 63021, USA
| | - Albert G Zimmermann
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, 125 Mason Farm Rd, Chapel Hill, NC 27599, USA
| | - Robert O Heuckeroth
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania and The Children's Hospital of Philadelphia Research Institute, 3615 Civic Center Blvd, Philadelphia, PA 19104, USA.
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Labesse G, Alexandre T, Gelin M, Haouz A, Munier-Lehmann H. Crystallographic studies of two variants ofPseudomonas aeruginosaIMPDH with impaired allosteric regulation. ACTA ACUST UNITED AC 2015; 71:1890-9. [DOI: 10.1107/s1399004715013115] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 07/07/2015] [Indexed: 11/10/2022]
Abstract
Inosine-5′-monophosphate dehydrogenases (IMPDHs), which are the rate-limiting enzymes in guanosine-nucleotide biosynthesis, are important therapeutic targets. Despite in-depth functional and structural characterizations of various IMPDHs, the role of the Bateman domain containing two CBS motifs remains controversial. Their involvement in the allosteric regulation ofPseudomonas aeruginosaIMPDH by Mg-ATP has recently been reported. To better understand the function of IMPDH and the importance of the CBS motifs, the structure of a variant devoid of these modules (ΔCBS) was solved at high resolution in the apo form and in complex with IMP. In addition, a single amino-acid substitution variant, D199N, was also structurally characterized: the mutation corresponds to the autosomal dominant mutant D226N of human IMPDH1, which is responsible for the onset of the retinopathy adRP10. These new structures shed light onto the possible mechanism of regulation of the IMPDH enzymatic activity. In particular, three conserved loops seem to be key players in this regulation as they connect the tetramer–tetramer interface with the active site and show significant modification upon substrate binding.
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40
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Du J, Linton JD, Hurley JB. Probing Metabolism in the Intact Retina Using Stable Isotope Tracers. Methods Enzymol 2015; 561:149-70. [PMID: 26358904 DOI: 10.1016/bs.mie.2015.04.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Vertebrate retinas have several characteristics that make them particularly interesting from a metabolic perspective. The retinas have a highly laminated structure, high energy demands, and they share several metabolic features with tumors, such as a strong Warburg effect and abundant pyruvate kinase M2 isoform expression. The energy demands of retinas are both qualitatively and quantitatively different in light and darkness and metabolic dysfunction could cause retinal degeneration. Stable isotope-based metabolic analysis with mass spectrometry is a powerful tool to trace the dynamic metabolic reactions and reveal novel metabolic pathways within cells and between cells in retina. Here, we describe methods to quantify retinal metabolism in intact retinas and discuss applications of these methods to the understanding of neuron-glia interaction, light and dark adaptation, and retinal degenerative diseases.
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Affiliation(s)
- Jianhai Du
- Departments of Biochemistry, University of Washington, Seattle, Washington, USA; Department of Ophthalmology, University of Washington, Seattle, Washington, USA
| | - Jonathan D Linton
- Departments of Biochemistry, University of Washington, Seattle, Washington, USA; Department of Ophthalmology, University of Washington, Seattle, Washington, USA
| | - James B Hurley
- Departments of Biochemistry, University of Washington, Seattle, Washington, USA; Department of Ophthalmology, University of Washington, Seattle, Washington, USA.
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Rizos E, Siafakas N, Katsantoni E, Skourti E, Salpeas V, Rizos I, Tsoporis JN, Kastania A, Filippopoulou A, Xiros N, Margaritis D, Parker TG, Papageorgiou C, Zoumpourlis V. Let-7, mir-98 and mir-183 as biomarkers for cancer and schizophrenia [corrected]. PLoS One 2015; 10:e0123522. [PMID: 25856466 PMCID: PMC4391828 DOI: 10.1371/journal.pone.0123522] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Accepted: 02/20/2015] [Indexed: 11/18/2022] Open
Abstract
Recent evidence supports a role of microRNAs in cancer and psychiatric disorders such as schizophrenia and bipolar disorder, through their regulatory role on the expression of multiple genes. The rather rare co-morbidity of cancer and schizophrenia is an old hypothesis which needs further research on microRNAs as molecules that might exert their oncosuppressive or oncogenic activity in the context of their role in psychiatric disorders. The expression pattern of a variety of different microRNAs was investigated in patients (N = 6) suffering from schizophrenia termed control, patients with a solid tumor (N = 10) and patients with both schizophrenia and tumor (N = 8). miRNA profiling was performed on whole blood samples using the miRCURY LNA microRNA Array technology (6th & 7th generation). A subset of 3 microRNAs showed a statistically significant differential expression between the control and the study groups. Specifically, significant down-regulation of the let-7p-5p, miR-98-5p and of miR-183-5p in the study groups (tumor alone and tumorand schizophrenia) was observed (p<0.05). The results of the present study showed that let-7, miR-98 and miR-183 may play an important oncosuppressive role through their regulatory impact in gene expression irrespective of the presence of schizophrenia, although a larger sample size is required to validate these results. Nevertheless, further studies are warranted in order to highlight a possible role of these and other micro-RNAs in the molecular pathways of schizophrenia.
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Affiliation(s)
- Emmanouil Rizos
- National and Kapodistrian University of Athens, Medical School, 2nd Department of Psychiatry, University “ATTIKON” General Hospital, Athens, Greece
- * E-mail:
| | - Nikolaos Siafakas
- National and Kapodistrian University of Athens, Medical School, Microbiology Laboratory, University “ATTIKON” General Hospital, Athens, Greece
| | - Eleni Katsantoni
- Biomedical Research Foundation, Academy of Athens, Hematology-Oncology Division, Athens, Greece
| | - Eleni Skourti
- Unit of Biomedical Applications, Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Vassilios Salpeas
- National & Kapodistrian University of Athens, 2nd Cardiology Department, University General Hospital “ATTIKON”, Athens, Greece
| | - Ioannis Rizos
- National & Kapodistrian University of Athens, 2nd Cardiology Department, University General Hospital “ATTIKON”, Athens, Greece
| | - James N. Tsoporis
- Keenan Research Centre. Li Ka Shing Knowledge Institute for Biomedical Science, St. Michael’s Hospital, Toronto, Canada
| | - Anastasia Kastania
- Department of Informatics, Athens University of Economics and Business, Athens, Greece
| | - Anastasia Filippopoulou
- National and Kapodistrian University of Athens, Medical School, 2nd Department of Psychiatry, University “ATTIKON” General Hospital, Athens, Greece
- Medical School, Democritus University of Thrace, University General Hospital of Alexandroupolis, Department of Psychiatry, Alexandroupolis, Greece
| | - Nikolaos Xiros
- Second Department of Propaedeutic Internal Medicine, Oncology Unit, Attikon University Hospital, Athens, Greece
| | - Demetrios Margaritis
- National and Kapodistrian University of Athens, Medical School, 2nd Department of Psychiatry, University “ATTIKON” General Hospital, Athens, Greece
| | - Thomas G. Parker
- Keenan Research Centre. Li Ka Shing Knowledge Institute for Biomedical Science, St. Michael’s Hospital, Toronto, Canada
| | - Charalabos Papageorgiou
- National and Kapodistrian University of Athens, Medical School, 2nd Department of Psychiatry, University “ATTIKON” General Hospital, Athens, Greece
| | - Vassilios Zoumpourlis
- Unit of Biomedical Applications, Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
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Nguyen ATH, Campbell M, Kiang AS, Humphries MM, Humphries P. Current therapeutic strategies for P23H RHO-linked RP. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 801:471-6. [PMID: 24664733 DOI: 10.1007/978-1-4614-3209-8_60] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The first autosomal dominant mutation identified to cause retinitis pigmentosa in the North American population was the substitution of proline to histidine at position 23 of the rhodopsin gene (P23H RHO). Many biochemical studies have demonstrated that P23H mutation induces rhodopsin (RHO) misfolding leading to endoplasmic reticulum stress. Herein, we review current thinking of this topic.
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Affiliation(s)
- Anh T H Nguyen
- The Ocular Genetics Unit, Smurfit Institute of Genetics, Trinity College Dublin, College Green, Dublin 2, Ireland,
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43
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MgATP regulates allostery and fiber formation in IMPDHs. Structure 2013; 21:975-85. [PMID: 23643948 DOI: 10.1016/j.str.2013.03.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 03/11/2013] [Accepted: 03/14/2013] [Indexed: 11/22/2022]
Abstract
Inosine-5'-monophosphate dehydrogenase (IMPDH) is a rate-limiting enzyme in nucleotide biosynthesis studied as an important therapeutic target and its complex functioning in vivo is still puzzling and debated. Here, we highlight the structural basis for the regulation of IMPDHs by MgATP. Our results demonstrate the essential role of the CBS tandem, conserved among almost all IMPDHs. We found that Pseudomonas aeruginosa IMPDH is an octameric enzyme allosterically regulated by MgATP and showed that this octameric organization is widely conserved in the crystal structures of other IMPDHs. We also demonstrated that human IMPDH1 adopts two types of complementary octamers that can pile up into isolated fibers in the presence of MgATP. The aggregation of such fibers in the autosomal dominant mutant, D226N, could explain the onset of the retinopathy adRP10. Thus, the regulatory CBS modules in IMPDHs are functional and they can either modulate catalysis or macromolecular assembly.
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Thomas EC, Gunter JH, Webster JA, Schieber NL, Oorschot V, Parton RG, Whitehead JP. Different characteristics and nucleotide binding properties of inosine monophosphate dehydrogenase (IMPDH) isoforms. PLoS One 2012; 7:e51096. [PMID: 23236438 PMCID: PMC3517587 DOI: 10.1371/journal.pone.0051096] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 10/29/2012] [Indexed: 11/18/2022] Open
Abstract
We recently reported that Inosine Monophosphate Dehydrogenase (IMPDH), a rate-limiting enzyme in de novo guanine nucleotide biosynthesis, clustered into macrostructures in response to decreased nucleotide levels and that there were differences between the IMPDH isoforms, IMPDH1 and IMPDH2. We hypothesised that the Bateman domains, which are present in both isoforms and serve as energy-sensing/allosteric modules in unrelated proteins, would contribute to isoform-specific differences and that mutations situated in and around this domain in IMPDH1 which give rise to retinitis pigmentosa (RP) would compromise regulation. We employed immuno-electron microscopy to investigate the ultrastructure of IMPDH macrostructures and live-cell imaging to follow clustering of an IMPDH2-GFP chimera in real-time. Using a series of IMPDH1/IMPDH2 chimera we demonstrated that the propensity to cluster was conferred by the N-terminal 244 amino acids, which includes the Bateman domain. A protease protection assay suggested isoform-specific purine nucleotide binding characteristics, with ATP protecting IMPDH1 and AMP protecting IMPDH2, via a mechanism involving conformational changes upon nucleotide binding to the Bateman domain without affecting IMPDH catalytic activity. ATP binding to IMPDH1 was confirmed in a nucleotide binding assay. The RP-causing mutation, R224P, abolished ATP binding and nucleotide protection and this correlated with an altered propensity to cluster. Collectively these data demonstrate that (i) the isoforms are differentially regulated by AMP and ATP by a mechanism involving the Bateman domain, (ii) communication occurs between the Bateman and catalytic domains and (iii) the RP-causing mutations compromise such regulation. These findings support the idea that the IMPDH isoforms are subject to distinct regulation and that regulatory defects contribute to human disease.
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Affiliation(s)
- Elaine C. Thomas
- Diamantina Institute for Cancer, Immunology and Metabolic Medicine, Princess Alexandra Hospital, University of Queensland, Brisbane, Queensland, Australia
- * E-mail: (ECT); (JPW)
| | - Jennifer H. Gunter
- Diamantina Institute for Cancer, Immunology and Metabolic Medicine, Princess Alexandra Hospital, University of Queensland, Brisbane, Queensland, Australia
| | - Julie A. Webster
- Diamantina Institute for Cancer, Immunology and Metabolic Medicine, Princess Alexandra Hospital, University of Queensland, Brisbane, Queensland, Australia
- Metabolic Medicine, Mater Medical Research Institute, South Brisbane, Queensland, Australia
| | - Nicole L. Schieber
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Viola Oorschot
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Robert G. Parton
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Jonathan P. Whitehead
- Diamantina Institute for Cancer, Immunology and Metabolic Medicine, Princess Alexandra Hospital, University of Queensland, Brisbane, Queensland, Australia
- Metabolic Medicine, Mater Medical Research Institute, South Brisbane, Queensland, Australia
- * E-mail: (ECT); (JPW)
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45
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Long MJC, Gollapalli DR, Hedstrom L. Inhibitor mediated protein degradation. ACTA ACUST UNITED AC 2012; 19:629-37. [PMID: 22633414 DOI: 10.1016/j.chembiol.2012.04.008] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 04/06/2012] [Accepted: 04/09/2012] [Indexed: 10/28/2022]
Abstract
The discovery of drugs that cause the degradation of their target proteins has been largely serendipitous. Here we report that the tert-butyl carbamate-protected arginine (Boc(3)Arg) moiety provides a general strategy for the design of degradation-inducing inhibitors. The covalent inactivators ethacrynic acid and thiobenzofurazan cause the specific degradation of glutathione-S-transferase when linked to Boc(3)Arg. Similarly, the degradation of dihydrofolate reductase is induced when cells are treated with the noncovalent inhibitor trimethoprim linked to Boc(3)Arg. Degradation is rapid and robust, with 30%-80% of these abundant target proteins consumed within 1.3-5 hr. The proteasome is required for Boc(3)Arg-mediated degradation, but ATP is not necessary and the ubiquitin pathways do not appear to be involved. These results suggest that the Boc(3)Arg moiety may provide a general strategy to construct inhibitors that induce targeted protein degradation.
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Affiliation(s)
- Marcus J C Long
- Graduate Program in Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
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Ouchida M, Kanzaki H, Ito S, Hanafusa H, Jitsumori Y, Tamaru S, Shimizu K. Novel direct targets of miR-19a identified in breast cancer cells by a quantitative proteomic approach. PLoS One 2012; 7:e44095. [PMID: 22952885 PMCID: PMC3431339 DOI: 10.1371/journal.pone.0044095] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 07/30/2012] [Indexed: 12/19/2022] Open
Abstract
The miR-17-92 cluster encodes 7 miRNAs inside a single polycistronic transcript, and is known as a group of oncogenic miRNAs that contribute to tumorigenesis in several cancers. However, their direct targets remain unclear, and it has been suggested that a single miRNA is capable of reducing the production of hundreds of proteins. The majority of reports on the identification of miRNA targets are based on computational approaches or the detection of altered mRNA levels, despite the fact that most miRNAs are thought to regulate their targets primarily by translational inhibition in higher organisms. In this study, we examined the target profiles of miR-19a, miR-20a and miR-92-1 in MCF-7 breast cancer cells by a quantitative proteomic strategy to identify their direct targets. A total of 123 proteins were significantly increased after the endogenous miR-19a, miR-20a and miR-92-1 were knocked down, and were identified as potential targets by two-dimensional electrophoresis and a mass spectrometric analysis. Among the upregulated proteins, four (PPP2R2A, ARHGAP1, IMPDH1 and NPEPL1) were shown to have miR-19a or miR-20a binding sites on their mRNAs. The luciferase activity of the plasmids with each binding site was observed to decrease, and an increased luciferase activity was observed in the presence of the specific anti-miRNA-LNA. A Western blot analysis showed the expression levels of IMPDH1 and NPEPL1 to increase after treatment with anti-miR-19a, while the expression levels of PPP2R2A and ARHGAP1 did not change. The expression levels of IMPDH1 and NPEPL1 did not significantly change by anti-miR-19a-LNA at the mRNA level. These results suggest that the IMPDH1 and NPEPL1 genes are direct targets of miR-19a in breast cancer, while the exogenous expression of these genes is not associated with the growth suppression of MCF-7 cells. Furthermore, our proteomic approaches were shown to be valuable for identifying direct miRNA targets.
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Affiliation(s)
- Mamoru Ouchida
- Department of Molecular Genetics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
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McGrew DA, Hedstrom L. Towards a Pathological Mechanism for IMPDH1-Linked Retinitis Pigmentosa. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 723:539-45. [DOI: 10.1007/978-1-4614-0631-0_68] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Tam LCS, Kiang AS, Campbell M, Keaney J, Farrar GJ, Humphries MM, Kenna PF, Humphries P. Protein Misfolding and Potential Therapeutic Treatments in Inherited Retinopathies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 723:567-72. [DOI: 10.1007/978-1-4614-0631-0_72] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Investigating the mechanism of disease in the RP10 form of retinitis pigmentosa. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011. [PMID: 20238057 DOI: 10.1007/978-1-4419-1399-9_62] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Retinitis pigmentosa (RP) is a disease characterized by its vast heterogeneity. Many genes are associated with RP, and the disease causing mutations identified in these genes are even more numerous. To date there are 15 genes that cause autosomal dominant RP (adRP) alone. The role of some of these genes, while complex and not completely understood, is somewhat intuitive in that they are involved in pathways such as phototransduction. However, the role of other genes in retinal disease is not as predictable due to their ubiquitous function and/or expression. One such gene is inosine monophosphate dehydrogenase 1 (IMPDH1) IMPDH1 is a gene involved in de novo purine synthesis and is ubiquitously expressed. IMPDH1 mutations account for 2% of all adRP cases and are a rare cause of Leiber Congenital Amaurosis. Despite its ubiquitous expression missense mutations in this gene cause only retinal degeneration. This paradox of tissue specific disease in the presence of ubiquitous expression has only recently begun to be explained. We have shown in a recent study that novel retinal isoforms of IMPDH1 exist and may account for the tissue specificity of disease. We have gone on to characterize these retinal isoforms both in our laboratory and in collaboration with Dr. Lizbeth Hedstrom's laboratory at Brandeis University (Waltham, MA) in order to understand more about them. We believe that through clarifying the mechanism of disease in RP10 we will be equipped to consider treatment options for this disease.
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Wang XT, Mion B, Aherne A, Engel PC. Molecular recruitment as a basis for negative dominant inheritance? propagation of misfolding in oligomers of IMPDH1, the mutated enzyme in the RP10 form of retinitis pigmentosa. Biochim Biophys Acta Mol Basis Dis 2011; 1812:1472-6. [PMID: 21791244 DOI: 10.1016/j.bbadis.2011.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 07/06/2011] [Accepted: 07/12/2011] [Indexed: 11/25/2022]
Abstract
Retinitis pigmentosa, causing progressive blindness, is genetically heterogeneous. RP10, due to a defect in inosine monophosphate dehydrogenase 1 (IMPDH1), shows autosomal dominant inheritance. Recombinantly expressed clinical mutants show unaltered kinetic behaviour. It is unclear why reportedly impaired DNA binding is important and how it would explain negative dominance. An alternative view relates to the mutant proteins' tendency to aggregate. Regarding negative dominance, a key question is whether the defective protein can subvert the function of its normal counterpart in the same cell. Potentially, the homotetrameric structure of IMPDH1 might offer a vehicle for such an effect. We have established a reliable protocol for reproducible refolding of recombinantly expressed IMPDH1 in vitro. Clinical mutants R224P and D226N both show impaired folding. For equimolar mixtures of normal and mutant enzymes, independent refolding would predict activity regain midway between pure mutant and pure normal. Under various conditions regain is close to the mutant figure, suggesting that, in hybrid tetramers, mutant subunits impose their faulty conformation on normal partners. The observed molecular recruitment is a negative counterpart of the intra-allelic complementation, also mediated via oligomeric structure and postulated many years ago by Fincham. These findings appear potentially to account for the negative dominant inheritance. This interpretation must be provisional at present, as the predominant transcript in retina is an alternatively spliced version not fully identical to that used in our study. The results nevertheless have a general significance in pointing to a mechanism for negative dominance that could be widespread.
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Affiliation(s)
- Xiao-Tao Wang
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Ireland.
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